Sequence
atgc intronic sequence ATGC exonic sequenceTATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaaaatttatgatagtcagtatc...
Basic information
species | Physcomitrella patens |
transcript | PP1S168_104V6.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatga-ttgagttgaaaatttatgatagtcagtatc-------------------------
||| |||||| || |||||||| |||||||| | ||||| ||||||||||| || || ||||| || ||||| |||||| ||||||| | | ||||||| || | | | | || || | | | ||| || | | | |||| ||| ||| ||| | || | |
CATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCTCCATAGCTGAGgtatg-----taggttattactattactgtgcacatggtttgactataatgttactatatgcagtattgaattgcacaacaaaaatgtggccatgcaaactgagcaatatcatcttaaatttacag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggt-----atcttgtgcaaagagtaatgattgagttgaa---aatttatgatagtcagtatc------------------------------------------------
||| | |||| ||| ||||| || |||||||| || ||||||||||| |||| || ||||||||||| |||||||| ||| ||||||| | | ||||||| ||| ||| | | | | | || || | | | || | | || || || || | || | | ||| | ||
CATTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCATTATGATGGGCCAAAGTTCCGCCTTGAGCTCTCCATCGCGGAGgtatattatgctgtcattatagaagaagttatggggggtagagtttgtttgtagatttggcccaggctgttttgttttctctatgtttcatctcataaagttgttgtccagatggtcatgtgaaccagttctcacgcacggaatttaaatctgcag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatca--------tatttaactcttaaac-acaaccgtccgcttcgt----tcagctcggtatcttgtgcaaagagtaatgattgagttgaaa--atttatgatagtcagtatc------
| | | |||| || ||| | || ||||| || || ||||||||||| ||||||| ||||||||||| ||||| |||||| |||| || ||||||||||||| | | | | |||||| | || | ||| | | | | | | | | |||| |||| ||| || || || | |||
TGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGATGGGCCAAAGTTTCGTCTTGAGCTGTCAGTTCCAGAGgtatgaaggaatgttgctatttttttaaactaaaaagaatcatttcatgacattgatttgtcaccgttggtttctgtctttgatggagtggaatttgttattgttattggatatattgcag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatca-----tatttaactcttaaac-----acaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaa--aatttatgatagtcagtatc----
| | | |||| || ||| | || ||||| || || ||||||||||| ||||||| ||||| ||||| ||||| |||||| | || || ||||||||||||| | |||| | |||||| | || | | | | | | | | | | |||| |||| ||| || || || | |||
TGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGACGGGCCAAAGTTTCGTCTTGAACTGTCAGTTCCAGAGgtatgaaggaatattgctattttaaactaaaaagaatcattccatgacattgatttgtccctgttggtttctgtcattgatggagtggaatttgttattgttattggatattgcag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA08G02840.2 (Glycine max), 5'ss of exon 3
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacac-aaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaaaatttatgatagtcagtatc----------------
| | | || ||| | || | || ||||| || ||||||||| | || || ||||||||||| ||||||||||||||| |||| ||| || ||||||| ||||| |||| | | | | | || | | | | | | || || | | | | || || |
AACTAGGAAAACTTGTGAACCACTGGAGGAGGATTCCTTCAGGCCAATCCTTCACCACTATGATGGTCCCAAGTTCCGTCTTGAGCTGAATGTGCCCGAGgtattttatttttatcttcttgattgaatattggtcccatttgaa--agaagataacatagttcatgttatttttttttctggtccactaaactctgtccctttttttggtttatag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA05G36700.1 (Glycine max), 5'ss of exon 4
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccg--tccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaaaatttatgatagtcagtatc---------------
| | | || ||| | || | || || || || ||||||||| | || || ||||||||||| ||||||||||||||| |||| ||| || ||||||| ||||| |||| | | | || || | || | || | || || | ||| || | | | | || | |
AACTAGGAAAACTTGTGAACCACTGGAGGAAGATTCCTTCAGGCCAATCCTTCACCACTATGATGGTCCCAAGTTCCGTCTTGAGCTGAATGTGCCCGAGgtattttatttttatcttgctgaatattggtcccatttgaaagaagatactaacatg-gttcagtgtttttattt--ttcctggtccactaaactctatccctttttgggtttatag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatg---attgagttgaaaatttatgatagtcagtatc---
| | || || || | || ||||||||||| ||||||||||| || || ||||||||||| || || ||||| ||| ||||||||||||| ||||| | | | | | | ||| | | || | || | | | | | |||| |||| || | | | ||| | | | |
AGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAGgtg-cgtgtccatatacgttttgtgaatgtcagt---aataagataattaagt-gaacggaaaataatctgtattgtgt-gtcatcatgtgaaaattggaacttgg
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 5
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgta--------tcatatttaactcttaaacacaaccgtccgct-tcgttcagctcggtatcttgtgcaaagagt-aatgattgagttgaaaatttatg-atagtcagtatc------------------------------------------------------
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TGTTAGGAACCTATGCAAGGCATTGGAGGAAGATGCTTTTAGGCCTGTCCTGCATCACTATGATGGACCTAAGTTCCGCCTTGAGCTTTCAGTTCCAGAGgtaaataagtgtcccaataagatttggtgtacaaatttttggggttgtaccttttctttttctttgcttatagttgaatatatatatatatatatatatacattaagcctagtgtttttattgtttgtatttattttgaactgagttttgttggtgattctgcag
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 4
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaaaatttatgatagtcagtatc------
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CACCAGGAAAATCTGTGAGCCAATGGAAGAGGATTCATTCAGGCCGGTCCTCCATCACTATGACGGCCCCAAGTTCCGCCTGGAGCTGAATGTGCCAGAGgta--aatctcaattc---aacaagatcaatcaatctagggag------atctcattaagggaacggcatcggattctgatgtgttttgttatctgaatttcacagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|22492594|gb|BU052517.1|BU052517EST: TGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAG GCTGGGGAGCTGCTGGATCTGTTCGAGGAGAATGGATCCCCTTAAGGGCTG
genomic: TGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatt ... gcctctccagGCTGTGGAGCTGCTGGATCTGTTCGAGGAGAATGGATCCCCTTAAGGGCTG
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATTCGAAAGCAGTGTAAGCCTTTAGAAGAGGACTCATTCAGGCCAGTGCTGCATCACTATGATGGGCCCAAGTTCCGTCTTCAGCTCTCTGTTCCAGAGgtatcatatttaactcttaaacacaaccgtccgcttcgttcagctcggtatcttgtgcaaagagtaatgattgagttgaaaatttatgatagtcagtatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacacaa